[med-svn] [Git][med-team/beagle][master] 2 commits: Standards-Version: 4.3.0 (no changes needed)
Dylan Aïssi
gitlab at salsa.debian.org
Thu Jul 4 07:11:54 BST 2019
Dylan Aïssi pushed to branch master at Debian Med / beagle
Commits:
82bfe2ec by Dylan Aïssi at 2019-07-04T06:02:31Z
Standards-Version: 4.3.0 (no changes needed)
- - - - -
5adf6940 by Dylan Aïssi at 2019-07-04T06:10:49Z
Update upstream docs
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/upstream.docs/README
- debian/upstream.docs/beagle_5.0.pdf
- debian/upstream.docs/run.beagle.example
Changes:
=====================================
debian/changelog
=====================================
@@ -1,6 +1,7 @@
beagle (5.0-190703+dfsg-1) UNRELEASED; urgency=medium
* New upstream release.
+ * Standards-Version: 4.3.0 (no changes needed).
-- Dylan Aïssi <daissi at debian.org> Thu, 04 Jul 2019 07:49:33 +0200
=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Build-Depends: debhelper (>= 11~),
javahelper
Build-Depends-Indep: default-jdk,
libhtsjdk-java
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/beagle
Vcs-Git: https://salsa.debian.org/med-team/beagle.git
Homepage: https://faculty.washington.edu/browning/beagle/beagle.html
=====================================
debian/upstream.docs/README
=====================================
@@ -1,10 +1,10 @@
-# Author: Dylan Assi <bob.dybian at gmail.com>
-# Last-Update: 2018-09-16
+# Author: Dylan Assi <daissi at debian.org>
+# Last-Update: 2019-07-04
# These files were downloaded from https://faculty.washington.edu/browning/beagle/
# They should be updated when upstream update them.
wget https://faculty.washington.edu/browning/beagle/beagle5_release_notes -O release_notes
- wget https://faculty.washington.edu/browning/beagle/beagle_5.0_07Sep18.pdf -O beagle_5.0.pdf
- wget https://faculty.washington.edu/browning/beagle/run.beagle.15Sep18.8a0.example -O run.beagle.example
- wget http://faculty.washington.edu/browning/beagle/test.15Sep18.8a0.vcf.gz -O test.vcf.gz && \
+ wget https://faculty.washington.edu/browning/beagle/beagle_5.0_03Jul19.pdf -O beagle_5.0.pdf
+ wget https://faculty.washington.edu/browning/beagle/run.beagle.03Jul19.b33.example -O run.beagle.example
+ wget http://faculty.washington.edu/browning/beagle/test.03Jul19.b33.vcf.gz -O test.vcf.gz && \
gunzip test.vcf.gz
=====================================
debian/upstream.docs/beagle_5.0.pdf
=====================================
Binary files a/debian/upstream.docs/beagle_5.0.pdf and b/debian/upstream.docs/beagle_5.0.pdf differ
=====================================
debian/upstream.docs/run.beagle.example
=====================================
@@ -1,47 +1,47 @@
#!/bin/bash
-if [ ! -f beagle.15Sep18.8a0.jar ]; then
+if [ ! -f beagle.03Jul19.b33.jar ]; then
echo
- echo "Downloading beagle.15Sep18.8a0.jar"
- wget http://faculty.washington.edu/browning/beagle/beagle.15Sep18.8a0.jar
+ echo "Downloading beagle.03Jul19.b33.jar"
+ wget http://faculty.washington.edu/browning/beagle/beagle.03Jul19.b33.jar
fi
-if [ ! -f bref3.15Sep18.8a0.jar ]; then
+if [ ! -f bref3.03Jul19.b33.jar ]; then
echo
- echo "Downloading bref3.15Sep18.8a0.jar"
- wget http://faculty.washington.edu/browning/beagle/bref3.15Sep18.8a0.jar
+ echo "Downloading bref3.03Jul19.b33.jar"
+ wget http://faculty.washington.edu/browning/beagle/bref3.03Jul19.b33.jar
fi
echo
-if [ ! -f test.15Sep18.8a0.vcf.gz ]; then
+if [ ! -f test.03Jul19.b33.vcf.gz ]; then
echo
- echo "*** Downloading some 1000 Genomes Project data to file: test.15Sep18.8a0.vcf.gz ***"
- wget http://faculty.washington.edu/browning/beagle/test.15Sep18.8a0.vcf.gz
+ echo "*** Downloading some 1000 Genomes Project data to file: test.03Jul19.b33.vcf.gz ***"
+ wget http://faculty.washington.edu/browning/beagle/test.03Jul19.b33.vcf.gz
fi
echo
-echo "*** Creating test files: ref.15Sep18.8a0.vcf.gz target.15Sep18.8a0.vcf.gz ***"
+echo "*** Creating test files: ref.03Jul19.b33.vcf.gz target.03Jul19.b33.vcf.gz ***"
echo
-zcat test.15Sep18.8a0.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.15Sep18.8a0.vcf.gz
-zcat test.15Sep18.8a0.vcf.gz | cut -f1-9,191-200 | gzip > target.15Sep18.8a0.vcf.gz
+zcat test.03Jul19.b33.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.03Jul19.b33.vcf.gz
+zcat test.03Jul19.b33.vcf.gz | cut -f1-9,191-200 | gzip > target.03Jul19.b33.vcf.gz
echo
echo "*** Running test analysis with \"gt=\" argument ***"
echo
-java -jar beagle.15Sep18.8a0.jar gt=test.15Sep18.8a0.vcf.gz out=out.gt
+java -jar beagle.03Jul19.b33.jar gt=test.03Jul19.b33.vcf.gz out=out.gt
echo
echo "*** Running test analysis with \"ref=\" and \"gt=\" arguments ***"
echo
-java -jar beagle.15Sep18.8a0.jar ref=ref.15Sep18.8a0.vcf.gz gt=target.15Sep18.8a0.vcf.gz out=out.ref
+java -jar beagle.03Jul19.b33.jar ref=ref.03Jul19.b33.vcf.gz gt=target.03Jul19.b33.vcf.gz out=out.ref
echo
echo "*** Making \"bref3\" file ***"
echo
-java -jar bref3.15Sep18.8a0.jar ref.15Sep18.8a0.vcf.gz > ref.15Sep18.8a0.bref3
+java -jar bref3.03Jul19.b33.jar ref.03Jul19.b33.vcf.gz > ref.03Jul19.b33.bref3
echo
echo "*** Running test analysis with \"bref3\" file ***"
echo
-java -jar beagle.15Sep18.8a0.jar ref=ref.15Sep18.8a0.bref3 gt=target.15Sep18.8a0.vcf.gz out=out.bref3
+java -jar beagle.03Jul19.b33.jar ref=ref.03Jul19.b33.bref3 gt=target.03Jul19.b33.vcf.gz out=out.bref3
View it on GitLab: https://salsa.debian.org/med-team/beagle/compare/f0089aa462b38c9cb6638a144a0424c52697106a...5adf6940dacbff22f6a846600017cc26778a95ef
--
View it on GitLab: https://salsa.debian.org/med-team/beagle/compare/f0089aa462b38c9cb6638a144a0424c52697106a...5adf6940dacbff22f6a846600017cc26778a95ef
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